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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
VirtualBox Resource Report Resource Website 50+ mentions |
VirtualBox (RRID:SCR_011876) | VirtualBox | software resource | A general-purpose full virtualizer for x86 and AMD64/Intel64 hardware, targeted at server, desktop and embedded use. | is listed by: OMICtools | GNU General Public License, v2 | OMICS_01208 | SCR_011876 | 2026-08-01 12:04:32 | 91 | |||||||||
|
GeneStitch Resource Report Resource Website |
GeneStitch (RRID:SCR_011910) | GeneStitch | software resource | Network Matching Algorithm using the de Bruijn graph assembly of metagenomes to improve the assembly of genes. | gene fragment, network matching, gene assembly, metagenomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Indiana University; Indiana; USA |
PMID:22962453 | Open unspecified license | OMICS_01421, biotools:genestitch | https://bio.tools/genestitch | SCR_011910 | GeneStitch: Network Matching Algorithm to Gene Assembly | 2026-08-01 12:04:33 | 0 | |||||
|
VMware Resource Report Resource Website 10+ mentions |
VMware (RRID:SCR_011878) | VMware | software resource | Software that virtualizes computing, from the data center to the cloud to mobile devices, to help customers be more agile, responsive, and profitable. | cloud, computing | is listed by: OMICtools | OMICS_01209 | SCR_011878 | 2026-08-01 12:04:31 | 21 | |||||||||
|
Genovo Resource Report Resource Website 100+ mentions |
Genovo (RRID:SCR_011911) | Genovo | software resource | Software for a novel de novo sequence assembler that discovers likely sequence reconstructions under the model. |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
OMICS_01422 | SCR_011911 | Genovo - Metagenomic de novo Sequencing | 2026-08-01 12:04:31 | 227 | |||||||||
|
DNAnexus Resource Report Resource Website 100+ mentions |
DNAnexus (RRID:SCR_011884) | DNAnexus | service resource | A cloud-based platform to support genomics at your organization. | genomics, cloud computing, genomic analysis | is listed by: OMICtools | OMICS_01217 | SCR_011884 | 2026-08-01 12:04:22 | 125 | |||||||||
|
Genestack Resource Report Resource Website 1+ mentions |
Genestack (RRID:SCR_011885) | Genestack | service resource | A universal collaborative platform for bioinformatics application development that allows users to store and share large data sets securely within and across organizations, with free access to public data from major databases. The platform includes open-source and proprietary genomics applications, working together independent of file formats. For developers an SDK, APIs and a marketplace are provided. | data sharing, data management, sequencing, quality control, exome, genome, variant call, somatic mutation, rna-seq, chip-seq, data analysis, visualization, computing, big data, next-generation sequencing | is listed by: OMICtools | OMICS_01218 | SCR_011885 | 2026-08-01 12:04:23 | 2 | |||||||||
|
Mega BLAST Resource Report Resource Website 100+ mentions |
Mega BLAST (RRID:SCR_011920) | Mega BLAST | software resource | Software that uses the greedy algorithm for nucleotide sequence alignment search. |
is listed by: OMICtools has parent organization: NCBI |
OMICS_01435 | SCR_011920 | 2026-08-01 12:04:25 | 280 | ||||||||||
|
UCLUST algorithm Resource Report Resource Website 50+ mentions |
UCLUST algorithm (RRID:SCR_011921) | UCLUST | software resource | Algorithm that divides a set of sequences into clusters | is listed by: OMICtools | PMID:20709691 | OMICS_01448 | SCR_011921 | 2026-08-01 12:04:31 | 50 | |||||||||
|
eXPatGen Resource Report Resource Website |
eXPatGen (RRID:SCR_011922) | eXPatGen | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A simulator of gene expression patterns in order to evaluate different analysis methods, such as clustering and principle component analysis (PCA). | is listed by: OMICtools | PMID:12801875 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01572 | SCR_011922 | eXPatGen - An On-line Gene Expression Pattern Generator | 2026-08-01 12:04:33 | 0 | |||||||
|
EBARDenovo Resource Report Resource Website 1+ mentions |
EBARDenovo (RRID:SCR_011890) | EBARDenovo | software resource | Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01317 | SCR_011890 | 2026-08-01 12:04:23 | 2 | ||||||||||
|
IDBA-Tran Resource Report Resource Website 10+ mentions |
IDBA-Tran (RRID:SCR_011891) | IDBA-Tran | software resource | An iterative De Bruijn Graph De Novo short read assembler for transcriptome. | is listed by: OMICtools | OMICS_01318 | SCR_011891 | 2026-08-01 12:04:33 | 25 | ||||||||||
|
RACER Resource Report Resource Website 10+ mentions |
RACER (RRID:SCR_011852) | RACER | software resource | A software program for correcting errors in sequencing data. | is listed by: OMICtools | OMICS_01108 | SCR_011852 | 2026-08-01 12:04:32 | 37 | ||||||||||
|
TIGRESS Resource Report Resource Website 1+ mentions |
TIGRESS (RRID:SCR_011977) | TIGRESS | software resource | Software providing a scoring technique for stability selection, which improves the performance of feature selection with LARS. TIGRESS can be run online through the GenePattern platform (GP-DREAM, http://dream.broadinstitute.org). | matlab |
is listed by: OMICtools is related to: GenePattern |
PMID:23173819 | OMICS_01687 | SCR_011977 | Trustful Inference of Gene REgulation using Stability Selection, TIGRESS: Trustful Inference of Gene REgulation using Stability Selection | 2026-08-01 12:04:26 | 9 | |||||||
|
NARWHAL Resource Report Resource Website 10+ mentions |
NARWHAL (RRID:SCR_011858) | NARWHAL | software resource | Automates the primary analysis of massive parallel sequencing data. |
is listed by: OMICtools has parent organization: Netherlands Bioinformatics Centre |
OMICS_01130 | SCR_011858 | 2026-08-01 12:04:21 | 10 | ||||||||||
|
orthAgogue Resource Report Resource Website 10+ mentions |
orthAgogue (RRID:SCR_011979) | orthAgogue | software resource | A software tool for high speed estimation of homology relations within and between species in massive data sets. | unix/linux |
is listed by: OMICtools has parent organization: Google Code |
PMID:24115168 | GNU General Public License, v3 | OMICS_01691 | SCR_011979 | orthAgogue: a tool for high speed estimation of homology relations within and between species in massive data sets. | 2026-08-01 12:04:34 | 31 | ||||||
|
SeqGene Resource Report Resource Website 1+ mentions |
SeqGene (RRID:SCR_011861) | SeqGene | software resource | An open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, etc. |
is listed by: OMICtools has parent organization: SourceForge |
Open unspecified license | OMICS_01134 | SCR_011861 | 2026-08-01 12:04:21 | 2 | |||||||||
|
Oqtans Resource Report Resource Website |
Oqtans (RRID:SCR_011905) | Oqtans | software resource | It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation as well as differential expression analysis. | windows, illumina | is listed by: OMICtools | Apache License | OMICS_01407 | SCR_011905 | Online Quantitative Transcriptome Analysis | 2026-08-01 12:04:33 | 0 | |||||||
|
reddit Resource Report Resource Website 50+ mentions |
reddit (RRID:SCR_011983) | software resource | A subreddit dedicated to bioinformatics, computational genomics and systems biology. | is listed by: OMICtools | OMICS_01708 | SCR_011983 | 2026-08-01 12:04:32 | 81 | |||||||||||
|
Genboree Workbench Resource Report Resource Website |
Genboree Workbench (RRID:SCR_011864) | Genboree | service resource | Service where users are able to upload and store data, access bioinformatics tools, and perform analyses. | metagenome, visualization, genome, transcriptiome, cistrome, epigenome, analysis, rna-seq, chip-seq |
is listed by: OMICtools has parent organization: Baylor University; Texas; USA |
Free for academic use | OMICS_01142 | SCR_011864 | 2026-08-01 12:04:30 | 0 | ||||||||
|
Ibis Resource Report Resource Website 10+ mentions |
Ibis (RRID:SCR_011865) | Ibis | software resource | An accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads. | is listed by: OMICtools | OMICS_01151 | SCR_011865 | Improved base identification system | 2026-08-01 12:04:22 | 47 |
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